Neuroimmunological diseases of the central nervous system (CNS) represent a broad spectrum of very diverse diagnoses, most of which are considered rare disorders. With the exception of multiple sclerosis (MS), acute demyelinating encephalomyelitis (ADEM), transverse myelitis (TM) and CNS lupus, reported cohorts in the literature rarely exceed 10-20 patients, and it takes years to collect these numbers. Additionally, with the exception of MS, virtually all reports focus on clinical findings and there is a great paucity of data characterizing intrathecal or systemic immune responses in these patients. As a result, the pathophysiology of these diseases is poorly understood and effective therapies are very rare. Emerging data indicate that the immune response is shaped not only by pathogens, but also by the tissue where the inflammatory process develops. From this standpoint, CNS tissue is unique. Elegant animal data indicate that foreign grafts survive indefinitely if transplanted into CNS tissue, bypassing systemic presentation of its antigens, whereas they are readily rejected when transplanted into other organs. Indeed, interactions of T cells with neurons can shape T cell effector phenotype, from pathogenic to more regulatory. There is little doubt that these complex immunoregulatory mechanisms emerged as an assurance that CNS tissue, which is vital for the function and survival of the host, will be protected from inadvertent damage by the immune system. Therefore, the apparent failure of the immune system that presents clinically as CNS autoimmunity may originate as a breakdown of natural immunoregulatory mechanisms that govern CNS-immune system interactions. This project studies intrathecal and systemic immune responses in patients referred to Neuroimmunological Diseases Unit (NDU) for diagnostic work-ups of neuroimmunological CNS disorders. The goal of this study is to define the pathophysiological mechanisms underlying the development of disability in immune-mediated disorders of the CNS and to distinguish these from physiological (and often beneficial) responses of the human immune system to CNS injury. We have established natural history protocol (09-N-0032) under which all untreated patients with suspected immune-mediated disorders of the CNS undergo detailed evaluation at NDU, consisting of the collection of clinical and paraclinical quantitative measures of disease activity and disability, standard and novel quantitative neuroimaging markers and immunological and molecular biomarkers originating from cerebrospinal fluid (CSF), serum and immune cells collected both from peripheral blood and CSF. Additionally, patients may undergo skin biopsy for collection of fibroblasts for their transformation into induced pluripotent stem (iPS) cells in order to develop autologous source of neural cells to study physiological neural-immune interactions in humans, which has not been possible thus far. All patients are coded and analysis of paraclinical, neuroimaging and molecular biomarkers are performed in an unbiased (i.e. blinded) fashion in order to define which biomarkers are associated with specific neuroimmunological disease or phenotype. The long-term objective of the study is to acquire knowledge that would allow us to therapeutically inhibit the pathogenic mechanisms and enhance repair mechanisms in immune-mediated CNS diseases, thereby minimizing the extent of CNS tissue damage and promoting recovery. Additionally, we expect that these studies will lead to the development of biomarkers and outcome measures (imaging, immunological and molecular) reflecting concurrent immune-mediated and neurodegenerative pathophysiological mechanisms and those that would able to distinguish among different diagnostic entities. This will lead to rational development and faster screening of process-specific therapies, and will permit the identification of patients with prevailing disease mechanisms, which is a requirement for a precision medicine. Ultimately, understanding the mechanisms of disease processes will impact the management of immune-mediated diseases of the CNS as a whole.